A pirate mission would be fitting. Upon completion you get an achievement, a pirate flagship, and maybe a title?
Mission: Win 500 battles as a pirate
For the pirate flagship, I think each pirate should have options. This is most simply done by letting him pick his flagship from any ship he owns. Said ship gets some nice perks for as long as that player flies the Jolly Roger. If the ship is sunk or stolen, the player can acquire another by completing the mission again just for the ship. Perks should be player specific though, not attached to the ship. Although maybe a trophy tag saying that the ship was formerly "Kakaroct's Flagship" would be warrented.
Now for the flagship itself..
My dream flagship would aid all my goals as a pirate. So a plunder bonus is a must. 10% at the max level seems worth the effort but not too much extra.
A small battle bonus would be sweet. Maybe 5-10% attack and defense bonus for the ship similar to bless and drums of war
I don't think any Levi protection would be fair. Same advantage / drawbacks to your shipchoice should apply.
Lastly maybe a travel speed perk for the ship's fleet.
On a side note, a mission of this sort for pirates would go really well with a ranking for notoriety. Maybe based on plunder won, and battle won, or better yet, update the fame system or make one for pirates. Titles could be available to parallel noble ranks. Pirate, Dread Pirate, Pirate King (a purely honorary title obviously)
My ten cents